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Fulltext Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence

Tan KY, Dutta A, Tan TK, Hari R, Othman RY, Choo SW

PeerJ, 2020;8:e9733.
PMID: 32953261 DOI: 10.7717/peerj.9733

Background: Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support.
Methodology: The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium's response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion.
Conclusion: This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.

Matched MeSH terms: Base Sequence
Occurrence of zoonotic Cryptosporidium and Giardia duodenalis species/genotypes in urban rodents

Tan TK, Low VL, Ng WH, Ibrahim J, Wang D, Tan CH, et al.

Parasitol Int, 2019 Apr;69:110-113.
PMID: 30590124 DOI: 10.1016/j.parint.2018.12.007

This report describes the detection of zoonotic Cryptosporidium muris, C. parvum subgenotype IIa and Giardia duodenalis genotype B in urban rodents in Malaysia. A rare occurrence of C. meleagridis was also reported suggesting a role of rodents in mechanical transmission of this pathogen. Utilization of DNA sequencing and subtyping analysis confirmed the presence of zoonotic C. parvum subtypes IIaA17G2R1 and IIaA16G3R1 for the first time in rodents.

Matched MeSH terms: Base Sequence
Structural approaches for the DNA binding motifs prediction in Bacillus thuringiensis sigma-E transcription factor (σETF)

Lim YY, Lim TS, Choong YS

J Mol Model, 2019 Sep 05;25(10):301.
PMID: 31486892 DOI: 10.1007/s00894-019-4192-3

The sigma-E transcription factor (σETF) can be found in most of the bacteria cells including Bacillus thuringiensis. However, the cellular regulatory mechanisms of these transcription factors in the mass production of δ-endotoxins during sporulation stage are yet to be revealed. In addition, the recognition of DNA towards σETF DNA binding motifs that led to the transcription activities is also being poorly studied. Therefore, this work studied the possible DNA binding motifs of σETF by utilising in silico approaches. The structure of σETF was first built via three different computational methods. A cognate DNA sequence was then docked to the predicted σETF DNA-binding motifs. The binding free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) for triplicate 50 ns simulation of σETF-DNA complex revealed favourable binding energy of DNA to σETF (average ∆Gbind = -34.57 kcal/mol) mainly driven by non-polar interactions. This study revealed that σETF LYS131, ARG133, PHE138, TRP146, ARG222, LYS225 and ARG226 are most likely the key residues upon the binding and recognition of DNA prior to transcription actives. Since determination of genome-regulating protein which recognises specific DNA sequence is important to discriminate between the proteins preferences for different genes, this study might provide some understanding on the possible σETF-DNA recognition prior to transcription initiated for the δ-endotoxins production.

Matched MeSH terms: Base Sequence
Fulltext Optimisation of biomass, exopolysaccharide and intracellular polysaccharide production from the mycelium of an identified Ganoderma lucidum strain QRS 5120 using response surface methodology

Supramani S, Ahmad R, Ilham Z, Annuar MSM, Klaus A, Wan-Mohtar WAAQI

AIMS Microbiol, 2019;5(1):19-38.
PMID: 31384700 DOI: 10.3934/microbiol.2019.1.19

Wild-cultivated medicinal mushroom Ganoderma lucidum was morphologically identified and sequenced using phylogenetic software. In submerged-liquid fermentation (SLF), biomass, exopolysaccharide (EPS) and intracellular polysaccharide (IPS) production of the identified G.lucidum was optimised based on initial pH, starting glucose concentration and agitation rate parameters using response surface methodology (RSM). Molecularly, the G. lucidum strain QRS 5120 generated 637 base pairs, which was commensurate with related Ganoderma species. In RSM, by applying central composite design (CCD), a polynomial model was fitted to the experimental data and was found to be significant in all parameters investigated. The strongest effect (p < 0.0001) was observed for initial pH for biomass, EPS and IPS production, while agitation showed a significant value (p < 0.005) for biomass. By applying the optimized conditions, the model was validated and generated 5.12 g/L of biomass (initial pH 4.01, 32.09 g/L of glucose and 102 rpm), 2.49 g/L EPS (initial pH 4, 24.25 g/L of glucose and 110 rpm) and 1.52 g/L of IPS (and initial pH 4, 40.43 g/L of glucose, 103 rpm) in 500 mL shake flask fermentation. The optimized parameters can be upscaled for efficient biomass, EPS and IPS production using G. lucidum.

Matched MeSH terms: Base Sequence
Fulltext Characterization of the mitogenomes of long-tailed giant rat, Leopoldamys sabanus and a comparative analysis with other Leopoldamys species

Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, et al.

Mitochondrial DNA B Resour, 2021 Feb 11;6(2):502-504.
PMID: 33628904 DOI: 10.1080/23802359.2021.1872433

Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanus has a typical vertebrate gene arrangement. Phylogenetic and BLASTn analysis using 10 Leopoldamys species mitogenomes revealed sequence variation occurred within species from different time zones. Along with the taxonomic issues, this suggests a landscape change might influence genetic connectivity.

Matched MeSH terms: Base Sequence
Fulltext The complete chloroplast genome and phylogenetic analysis of Nephelium lappaceum (rambutan)

Liu J, Zheng C, Liu ZY, Niu YF

Mitochondrial DNA B Resour, 2021 Feb 09;6(2):485-487.
PMID: 33628898 DOI: 10.1080/23802359.2021.1872449

Nephelium lappaceum is a popular tropical fruit belonging to the Sapindaceae family. The plant originated in Malaysia and Indonesia and is commonly called rambutan. Because of its refreshing flavor and exotic appearance, rambutan is widely accepted in the World. Due to its significant medicinal properties, the fruit has also been employed in traditional medicine for centuries. The chloroplast genome of rambutan was sequenced, assembled, and annotated in the present study. The chloroplast genome length was 161,356 bp and contained 132 genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. It possessed the typical quadripartite circle structure with a large single-copy region (86,009 bp), a small single-copy region (18,153 bp), and two inverted repeat regions (28,597 bp). A total of 35 SSR markers were found in the chloroplast genome of Nephelium lappaceum, of which 33 were monomer, 1 was dimer and 1 was tetramer. Phylogenetic analysis based on the complete chloroplast genome sequences of 21 plant species showed that rambutan was closely related to Pometia tomentosa. These results provide a foundation for further phylogenetic and evolutionary studies of the Sapindaceae family.

Matched MeSH terms: Base Sequence
Fulltext Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida

Huertas-Rosales Ó, Romero M, Chan KG, Hong KW, Cámara M, Heeb S, et al.

Front Mol Biosci, 2021;8:624061.
PMID: 33693029 DOI: 10.3389/fmolb.2021.624061

Post-transcriptional regulation is an important step in the control of bacterial gene expression in response to environmental and cellular signals. Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences bound in vivo by each of these proteins. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to discover direct binding targets, corresponding to 437 unique RNA molecules, 75 of them being common to the three proteins. Relevant targets include genes encoding proteins involved in signal transduction and regulation, metabolism, transport and secretion, stress responses, and the turnover of the intracellular second messenger c-di-GMP. To our knowledge, this is the first combined global analysis in a bacterium harboring three Rsm homologs. It offers a broad overview of the network of processes subjected to this type of regulation and opens the way to define what are the sequence and structure determinants that define common or differential recognition of specific RNA molecules by these proteins.

Matched MeSH terms: Base Sequence
Fulltext Comparing the genomes of Helicobacter pylori clinical strain UM032 and Mice-adapted derivatives

Khosravi Y, Rehvathy V, Wee WY, Wang S, Baybayan P, Singh S, et al.

Gut Pathog, 2013;5:25.
PMID: 23957912 DOI: 10.1186/1757-4749-5-25

Helicobacter pylori is a Gram-negative bacterium that persistently infects the human stomach inducing chronic inflammation. The exact mechanisms of pathogenesis are still not completely understood. Although not a natural host for H. pylori, mouse infection models play an important role in establishing the immunology and pathogenicity of H. pylori. In this study, for the first time, the genome sequences of clinical H. pylori strain UM032 and mice-adapted derivatives, 298 and 299, were sequenced using the PacBio Single Molecule, Real-Time (SMRT) technology.

Matched MeSH terms: Base Sequence
Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae)

Kodada J, Jäch MA, Freitag H, Čiamporová-Zaťovičová Z, Goffová K, Selnekovič D, et al.

Zookeys, 2020;1003:31-55.
PMID: 33384561 DOI: 10.3897/zookeys.1003.55541

Ancyronyx lianlabangorumsp. nov. (Coleoptera, Elmidae), a new spider riffle beetle from the Kelabit Highlands (Sarawak, northern Borneo), is described. Illustrations of the habitus and diagnostic characters of the new species and the similar, polymorphic A. pulcherrimus Kodada et al. are presented. Differences to closely related species, based on COI nucleotide sequences and morphological characters, are discussed. Ancyronyx pulcherrimus is here recorded from Sarawak for the first time, based on DNA barcoding.

Matched MeSH terms: Base Sequence
Fulltext Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4

Gan HM, Lee MVL, Savka MA

PeerJ, 2019;7:e6366.
PMID: 30775173 DOI: 10.7717/peerj.6366

The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.

Matched MeSH terms: Base Sequence
Fulltext Targeted DNA complementation on a 1,1'-carbonyldiimidazole-functionalized surface for identifying Mycobacterium tuberculosis

Xu S, Xue Y, Guo F, Xu M, Gopinath SCB, Mao X

3 Biotech, 2020 May;10(5):227.
PMID: 32373419 DOI: 10.1007/s13205-020-02216-2

Herein, a rapid and sensitive current-volt measurement was developed for identifying the IS6110 DNA sequence to diagnose Mycobacterium tuberculosis (TB). An aminated capture probe was immobilized on a 1,1'-carbonyldiimidazole-functionalized interdigitated electrode (IDE) silica substrate, and the target sequence was detected by complementation. It was found that all tested concentrations displayed a higher response in current changes than the control, and the limit of detection was 10 fM. The sensitivity ranged from 1 to 10 fM. The control sequences with single-, triple-mismatch and noncomplementary sequences showed great discrimination. This rapid and easy DNA detection method helps to identify M. tuberculosis for early-stage diagnosis of TB.

Matched MeSH terms: Base Sequence
Fulltext Characterization of the complete mitochondrial genome of Xanthid crab, Atergatis integerrimus from China (Decapoda: Brachyura) and its phylogenetic analysis

Xie Z, Tan H, Lin F, Guan M, Waiho K, Fang S, et al.

Mitochondrial DNA B Resour, 2018 Mar 27;3(1):397-398.
PMID: 33474181 DOI: 10.1080/23802359.2018.1456374

The complete mitochondrial genome sequence of Atergatis integerrimus from China has been amplified and sequenced in this study. The mitogenome assembly was found to be 15,924 bp in length with base composition of A (32.88%), G (10.58%), C (20.87%), T (35.66%), A + T (68.54%), and G + C (31.46%). It contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The phylogenetic position was constructed and the A. integerrimus was closely clustered with Pseudocarcinus gigas and Leptodius sanguineus. The complete mitochondrial genome sequence would be useful for further understanding the evolution of A. integerrimus.

Matched MeSH terms: Base Sequence
Fulltext Complete mitochondrial genome of six Cheilinus undulatus (Napoleon Wrasse): an endangered marine fish species from Sabah, Malaysia

Matthew P, Manjaji-Matsumoto BM, Rodrigues KF

Mitochondrial DNA B Resour, 2018 Oct 12;3(2):943-944.
PMID: 33474374 DOI: 10.1080/23802359.2018.1473725

We report here the complete mitochondrial (mt) genomes of six individuals of Cheilinus undulatus (Napoleon Wrasse), an endangered marine fish species. The six mt DNA sequences had an average size of 17,000 kb and encoded 22 tRNA, two sRNA, 13 highly conserved protein coding genes and a control region. The polymorphic variation (control region) in these six individuals suggests their potential use as a specific marker for phylogeographic conservation. Moreover, the sequence polymorphism within the control region (D-loop) suggests that this locus can be applied for phylogenetic studies.

Matched MeSH terms: Base Sequence
Fulltext Draft Genome Sequence of a Vibrio parahaemolyticus Strain, KS17.S5-1, with Multiple Antibiotic Resistance Genes, Which Causes Acute Hepatopancreatic Necrosis Disease in Penaeus monodon in the West Coast of Peninsular Malaysia

Devadas S, Bhassu S, Christie Soo TC, Mohamed Iqbal SN, Yusoff FM, Shariff M

Microbiol Resour Announc, 2018 Jul;7(2).
PMID: 30533806 DOI: 10.1128/MRA.00829-18

We report the first draft genome sequence of a Vibrio parahaemolyticus strain (VpAHPND), which causes acute hepatopancreatic necrosis disease (AHPND) in Penaeus monodon. The strain has a pVA1-like plasmid carrying pirAvp and pirBvp genes. Whole-genome comparisons revealed >98% similarity to VpAHPND isolates from Thailand, Mexico, and Vietnam.

Matched MeSH terms: Base Sequence
Fulltext Draft Genome Sequence of the Phenol-Degrading Bacterium Cupriavidus sp. Strain P-10, Isolated from Trichloroethene-Contaminated Aquifer Soil

Suzuki K, Aziz FAA, Honjo M, Nishimura T, Masuda K, Minoura A, et al.

Microbiol Resour Announc, 2018 Nov;7(18).
PMID: 30533775 DOI: 10.1128/MRA.01009-18

A batch culture was enriched on phenol with trichloroethene-contaminated aquifer soil as an inoculum. Cupriavidus sp. strain P-10 was isolated from the culture using a diluted plating method. Here, we report the draft genome sequence and annotation of strain P-10, which provides insights into the metabolic processes of phenol degradation.

Matched MeSH terms: Base Sequence
Fulltext Draft Genome Sequence of the Shrimp Pathogen Vibrio parahaemolyticus ST17.P5-S1, Isolated in Peninsular Malaysia

Devadas S, Bhassu S, Christie Soo TC, Yusoff FM, Shariff M

Microbiol Resour Announc, 2018 Sep;7(11).
PMID: 30533648 DOI: 10.1128/MRA.01053-18

We sequenced the genome of Vibrio parahaemolyticus strain ST17.P5-S1, isolated from Penaeus vannamei cultured in the east coast of Peninsular Malaysia. The strain contains several antibiotic resistance genes and a plasmid encoding the Photorhabdus insect-related (Pir) toxin-like genes, pirAvp and pirBvp, associated with acute hepatopancreatic necrosis disease (AHPND).

Matched MeSH terms: Base Sequence
Fulltext Whole-Genome Shotgun Sequence of Streptococcus agalactiae Sequence Type 176 Strain 3966RFQB from a Dairy Herd in Selangor, Malaysia

Bashir A, Zunita Z, Jesse FFA, Ramanoon SZ

Microbiol Resour Announc, 2019 Feb;8(6).
PMID: 30746526 DOI: 10.1128/MRA.01618-18

Streptococcus agalactiae, commonly known as group B streptococcus (GBS), is among the most implicated pathogens in bovine mastitis worldwide. Proper control measures can curb both economic and public health effects it may cause. Here, we report the sequenced genome of S. agalactiae sequence type 167 (ST167) strain 3966RFQB obtained from a bovine mastitis case at a dairy herd in Banting, Selangor, Malaysia (longitude 2.8121°N, latitude 101.5026°E).

Matched MeSH terms: Base Sequence
Fulltext Draft Genome Sequence of the Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolate INF13/18/A, Recovered from Kelantan, Malaysia

Wan Makhtar WR, Mohd Azlan M, Hassan NH, Aziah I, Samsurizal NH, Yusof NY

Microbiol Resour Announc, 2020 Aug 13;9(33).
PMID: 32817162 DOI: 10.1128/MRA.01497-19

We describe here the draft genome sequence and basic characteristics of Escherichia coli isolate INF13/18/A, which was isolated from Universiti Sains Malaysia (USM) Hospital. This isolate was identified as an extended-spectrum β-lactamase-producing Escherichia coli strain harboring the antimicrobial resistance genes TEM, CTX-M-1, and CTX-M-9.

Matched MeSH terms: Base Sequence
Fulltext Phylogeny of Algal Sequences Encoding Carbohydrate Sulfotransferases, Formylglycine-Dependent Sulfatases, and Putative Sulfatase Modifying Factors

Ho CL

Front Plant Sci, 2015;6:1057.
PMID: 26635861 DOI: 10.3389/fpls.2015.01057

Many algae are rich sources of sulfated polysaccharides with biological activities. The physicochemical/rheological properties and biological activities of sulfated polysaccharides are affected by the pattern and number of sulfate moieties. Sulfation of carbohydrates is catalyzed by carbohydrate sulfotransferases (CHSTs) while modification of sulfate moieties on sulfated polysaccharides was presumably catalyzed by sulfatases including formylglycine-dependent sulfatases (FGly-SULFs). Post-translationally modification of Cys to FGly in FGly-SULFs by sulfatase modifiying factors (SUMFs) is necessary for the activity of this enzyme. The aims of this study are to mine for sequences encoding algal CHSTs, FGly-SULFs and putative SUMFs from the fully sequenced algal genomes and to infer their phylogenetic relationships to their well characterized counterparts from other organisms. Algal sequences encoding CHSTs, FGly-SULFs, SUMFs, and SUMF-like proteins were successfully identified from green and brown algae. However, red algal FGly-SULFs and SUMFs were not identified. In addition, a group of SUMF-like sequences with different gene structure and possibly different functions were identified for green, brown and red algae. The phylogeny of these putative genes contributes to the corpus of knowledge of an unexplored area. The analyses of these putative genes contribute toward future production of existing and new sulfated carbohydrate polymers through enzymatic synthesis and metabolic engineering.

Matched MeSH terms: Base Sequence
Fulltext The whole mitochondrial genome of the mangrove crab, Metopograpsus frontalis (Miers, 1880) (Decapoda, Grapsidae) and its phylogenetic relationship

Guan M, Liu X, Lin F, Xie Z, Fazhan H, Ikhwanuddin M, et al.

Mitochondrial DNA B Resour, 2018 Mar 14;3(1):368-369.
PMID: 33490509 DOI: 10.1080/23802359.2018.1450685

In this study, we sequenced and analyzed the whole mitochondrial genome of Metopograpsus frontalis Miers, 1880 (Decapoda, Grapsidae). The circular genome is 15,587 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, as well as a control region. Both atp8/atp6 and nad4L/nad4 share 7 nucleotides in their adjacent overlapping region, which is identical to those observed in other Grapsidae crabs. The genome composition and gene order follow a classic crab-type arrangement regulation. The phylogenetic analysis suggested that Grapsidae crabs formed a solid monophyletic group. The newly described mitochondrial genome may provide genetic marker for studies on phylogeny of the grapsid crabs.

Matched MeSH terms: Base Sequence

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