NDLI: Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes

Content Provider	Springer Nature : BioMed Central
Author	Mukherjee, Mishtu Vajpai, Manu Sankararamakrishnan, Ramasubbu
Abstract	Background The monovalent anions formate, nitrite and hydrosulphide are main metabolites of bacterial respiration during anaerobic mixed-acid fermentation. When accumulated in the cytoplasm, these anions become cytotoxic. Membrane proteins that selectively transport these monovalent anions across the membrane have been identified and they belong to the family of Formate/Nitrite Transporters (FNTs). Individual members that selectively transport formate, nitrite and hydrosulphide have been investigated. Experimentally determined structures of FNTs indicate that they share the same hourglass helical fold with aquaporins and aquaglyceroporins and have two constriction regions, namely, cytoplasmic slit and central constriction. Members of FNTs are found in bacteria, archaea, fungi and protists. However, no FNT homolog has been identified in mammals. With FNTs as potential drug targets for many bacterial diseases, it is important to understand the mechanism of selectivity and transport across these transporters. Results We have systematically searched the sequence databases and identified 2206 FNT sequences from bacteria, archaea and eukaryotes. Although FNT sequences are very diverse, homology modeling followed by structure-based sequence alignment revealed that nearly one third of all the positions within the transmembrane region exhibit high conservation either as a group or at the level of individual residues across all three kingdoms. Phylogenetic analysis of prokaryotic FNT sequences revealed eight different subgroups. Formate, nitrite and hydrosulphide transporters respectively are clustered into two (FocA and FdhC), three (NirC-α, NirC-β and NirC-γ) and one (HSC) subfamilies. We have also recognized two FNT subgroups (YfdC-α and YfdC-β) with unassigned function. Analysis of taxonomic distribution indicates that each subfamily prefers specific taxonomic groups. Structure-based sequence alignment of individual subfamily members revealed that certain positions in the two constriction regions and some residues facing the interior show subfamily-specific conservation. We have also identified examples of FNTs with the two constriction regions formed by residues that are less frequently observed. We have developed dbFNT, a database of FNT models and associated details. dbFNT is freely available to scientific community. Conclusions Taxonomic distribution and sequence conservation of FNTs exhibit subfamily-specific features. The conservation pattern in the central constriction and cytoplasmic slit in the open and closed states are distinct for YfdC and NirC subfamilies. The same is true for some residues facing the interior of the transporters. The specific residues in these positions can exert influence on the type of solutes that are transported by these proteins. With FNTs found in many disease-causing bacteria, the knowledge gained in this study can be used in the development and design of anti-bacterial drugs.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-017-3947-4.pdf
Ending Page	19
Page Count	19
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-017-3947-4
Journal	BMC Genomics
Issue Number	1
Volume Number	18
Language	English
Publisher	BioMed Central
Publisher Date	2017-07-24
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Anion transport Structure-based sequence alignment FNT family Channel selectivity and transport Phylogenetic analysis Hour-glass helical fold Sequence diversity Homology modeling Gating Conformational changes
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

Unraveling the substrate preference of an uncharacterized phylogenetic subgroup in Formate/Nitrite Transporter (FNT) family: Computational studies of anion transport in Escherichia coli FNT homolog

Phylogenetic, syntenic, and tissue expression analysis of slc22 genes in zebrafish (Danio rerio)

Sequence alignment by passing messages

Mutational widening of constrictions in a formate-nitrite/H⁺ transporter enables aquaporin-like water permeability and proton conductance.

Energetics and mechanism of anion permeation across formate-nitrite transporters

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

Census-based rapid and accurate metagenome taxonomic profiling

Scaling statistical multiple sequence alignment to large datasets

Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes

Similar Documents

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

Unraveling the substrate preference of an uncharacterized phylogenetic subgroup in Formate/Nitrite Transporter (FNT) family: Computational studies of anion transport in Escherichia coli FNT homolog

Phylogenetic, syntenic, and tissue expression analysis of slc22 genes in zebrafish (Danio rerio)

Sequence alignment by passing messages

Mutational widening of constrictions in a formate-nitrite/H+ transporter enables aquaporin-like water permeability and proton conductance.

Energetics and mechanism of anion permeation across formate-nitrite transporters

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

Census-based rapid and accurate metagenome taxonomic profiling

Scaling statistical multiple sequence alignment to large datasets

Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes

Mutational widening of constrictions in a formate-nitrite/H⁺ transporter enables aquaporin-like water permeability and proton conductance.