Comparative genomic analysis of <i>Citrobacter</i> sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals

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Abstract

Background

In our previous study, Citrobacter sp. XT1-2-2 was isolated from high cadmium-contaminated soils, and demonstrated an excellent ability to decrease the bioavailability of cadmium in the soil and inhibit cadmium uptake in rice. In addition, the strain XT1-2-2 could significantly promote rice growth and increase rice biomass. Therefore, the strain XT1-2-2 shows great potential for remediation of cadmium -contaminated soils. However, the genome sequence of this organism has not been reported so far.

Results

Here the basic characteristics and genetic diversity of the strain XT1-2-2 were described, together with the draft genome and comparative genomic results. The strain XT1-2-2 is 5040459 bp long with an average G + C content of 52.09%, and contains a total of 4801 genes. Putative genomic islands were predicted in the genome of Citrobacter sp. XT1-2-2. All genes of a complete set of sulfate reduction pathway and various putative heavy metal resistance genes in the genome were identified and analyzed.

Conclusions

These analytical results provide insights into the genomic basis of microbial immobilization of heavy metals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-09069-4.

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Most cited references 40

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KEGG: kyoto encyclopedia of genes and genomes.

M Kanehisa (2000)

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).

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Toward understanding the origin and evolution of cellular organisms

Minoru Kanehisa (2019)

In this era of high‐throughput biology, bioinformatics has become a major discipline for making sense out of large‐scale datasets. Bioinformatics is usually considered as a practical field developing databases and software tools for supporting other fields, rather than a fundamental scientific discipline for uncovering principles of biology. The KEGG resource that we have been developing is a reference knowledge base for biological interpretation of genome sequences and other high‐throughput data. It is now one of the most utilized biological databases because of its practical values. For me personally, KEGG is a step toward understanding the origin and evolution of cellular organisms.

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Is Open Access

KEGG: integrating viruses and cellular organisms

Minoru Kanehisa, Miho Furumichi, Yoko Sato … (2020)

Abstract KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and organism-level functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular network systems from molecular building blocks based on the concept of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with network variants, which are perturbed molecular networks caused by human gene variants, viruses, other pathogens and environmental factors. The network variation maps are created as aligned sets of related networks showing, for example, how different viruses inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation maps in the NETWORK database, as well as with conserved functional units of KEGG modules and reaction modules in the MODULE database. The KO database for functional orthologs continues to be improved and virus KOs are being expanded for better understanding of virus-cell interactions and for enabling prediction of viral perturbations.

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Author and article information

Contributors

Min Zhang: 178488510@qq.com

Dongxia Du: xiaxia414@126.com

Zhaohui Guo: 157263033@qq.com

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 19 December 2022

Publication date PMC-release: 19 December 2022

Publication date Collection: 2022

Volume: 23

Electronic Location Identifier: 838

Affiliations

[1 ]GRID grid.506983.1, Hunan Institute of Microbiology, ; 410009 Changsha, Hunan China

[2 ]Hunan Engineering and Technology Research Center of Agricultural Microbiology Application, 410009 Changsha, Hunan China

Article

Publisher ID: 9069

DOI: 10.1186/s12864-022-09069-4

PMC ID: 9764585

PubMed ID: 36536293

SO-VID: bbb65fd7-23ee-4932-9744-637f57c2d8ea

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 12 May 2022

Date accepted : 5 December 2022

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 32171633

Funded by: Natural Science Foundation of Hunan Province of China

Award ID: 2021JJ40307

Funded by: Key Technology Research Project of Hunan Province of China

Award ID: 2021NK1040

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: citrobacter,cadmium,microbial immobilization,rice,sulfate reduction pathway

Data availability:

ScienceOpen disciplines: Genetics

Keywords: citrobacter, cadmium, microbial immobilization, rice, sulfate reduction pathway

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Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals

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Abstract

Background

Results

Conclusions

Supplementary Information

Related collections

Genome Integrity

Most cited references 40

KEGG: kyoto encyclopedia of genes and genomes.

Toward understanding the origin and evolution of cellular organisms

KEGG: integrating viruses and cellular organisms

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