6TMS neutral amino acid transporter family

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The 6TMS Neutral Amino Acid Transporter (NAAT) Family (TC# 2.A.95) is a family of transporters belonging to the Lysine Exporter (LysE) Superfamily. Homologues are found in numerous Gram-negative and Gram-positive bacteria including many human pathogens. Several archaea also encode MarC (see below) homologues. Some of these organisms have 2 or more paralogues. Most of these proteins are of about the same size (180-230 aas) although a few are larger. They exhibit 6 (or in some cases, possibly 5) putative TMSs. A representative list of members belonging to the NAAT family can be found in the Transporter Classification Database.

Contents

SnatA

A gene encoding a small neutral amino acid transporter was cloned from the genome of the hyperthermophilic archaeon Thermococcus sp. KS-1. The cloned gene, snatA, encodes a protein of 216 amino acid residues, SnatA (TC# 2.A.95.1.4), with six membrane-spanning segments (TMSs). Competition studies indicated that SnatA transports various L-type neutral amino acids. It has also been noted that glycine transport is inhibited by a protonophore, FCCP, or valinomycin plus nigericin, indicating that the process is dependent on an electrochemical potential of H+. [1]

The generalized reaction catalyzed by SnatA is: [2]

Amino acid (in) → Amino acid (out)

MarC

MarC is encoded by a gene at the multiple antibiotic resistance (mar) locus. The mar locus consists of two divergently positioned transcriptional units that flank the operator, marO, in both E. coli and Salmonella typhimurium. One transcription unit encodes MarC, an integral inner membrane protein with 6 established TMSs with the N- and C-termini in the cytoplasm. [3] Its function is unknown. The other unit consists of an operon, marRAB, encoding (1) the MarR repressor which binds marO and negatively regulates marRAB expression, (2) MarA, a transcriptional activator that activates expression of other genes such as acrAB (encoding the principal E. coli multidrug efflux pump of the RND superfamily (TC #2.A.6.2)) and the mar regulon itself, and (3) MarB, a small protein of 71 amino acyl residues of unknown function. A periplasmic binding protein, MppA, essential for the uptake of the cell wall murein tripeptide, L-alanyl-γ-D-glutamyl-meso-diaminopimelate via the Opp permease, regulates mar regulon expression. Loss of MppA causes overproduction of MarA which activates acrAB, causing pleiotropic drug resistance. MppA probably functions upstream of MarA in a signal transduction pathway that negatively controls expression of the marRAB operon.

Related Research Articles

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Amino acid synthesis is the set of biochemical processes by which the amino acids are produced. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. For example, humans can only synthesize 11 of the 20 standard amino acids, and in time of accelerated growth, histidine can be considered an essential amino acid.

The sodium/phosphate cotransporter is a member of the phosphate:Na+ symporter (PNaS) family within the TOG Superfamily of transport proteins as specified in the Transporter Classification Database (TCDB).

Caldococcus is a genus of Archaea in the order Desulfurococcales.

The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily. FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea, yeast, plants and lower eukaryotes. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.

The Nucleobase cation symporter-2 (NCS2) family, also called the Nucleobase ascorbate transporter (NAT) family, consists of over 1000 sequenced proteins derived from gram-negative and gram-positive bacteria, archaea, fungi, plants and animals. The NCS2/NAT family is a member of the APC Superfamily of secondary carriers. Of the five known families of transporters that act on nucleobases, NCS2/NAT is the only one that is most widespread. Many functionally characterized members are specific for nucleobases including both purines and pyrimidines, but others are purine-specific. However, two closely related rat/human members of the family, SVCT1 and SVCT2, localized to different tissues of the body, co-transport L-ascorbate (vitamin C) and Na+ with a high degree of specificity and high affinity for the vitamin. Clustering of NCS2/NAT family members on the phylogenetic tree is complex, with bacterial proteins and eukaryotic proteins each falling into at least three distinct clusters. The plant and animal proteins cluster loosely together, but the fungal proteins branch from one of the three bacterial clusters forming a tighter grouping. E. coli possesses four distantly related paralogous members of the NCS2 family.

Mercury transporter group of transport proteins

The mercury transporter superfamily is a family of transmembrane bacterial transporters of mercury ions. The common origin of all Mer superfamily members has been established. The common elements between family members are included in TMSs 1-2. A representative list of the subfamilies and proteins that belong to those subfamilies is available in the Transporter Classification Database.

The amino acid-polyamine-organocation (APC) superfamily is the second largest superfamily of secondary carrier proteins currently known, and it contain several Solute carriers. Originally, the APC superfamily consisted of subfamilies under the transporter classification number 2.A.3. This superfamily has since been expanded to include eighteen different families.

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The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase superfamily is a group of integral membrane protein families. The MOP flippase superfamily includes twelve distantly related families, six for which functional data are available:

  1. One ubiquitous family (MATE) specific for drugs - (TC# 2.A.66.1) The Multi Antimicrobial Extrusion (MATE) Family
  2. One (PST) specific for polysaccharides and/or their lipid-linked precursors in prokaryotes - (TC# 2.A.66.2) The Polysaccharide Transport (PST) Family
  3. One (OLF) specific for lipid-linked oligosaccharide precursors of glycoproteins in eukaryotes - (TC# 2.A.66.3) The Oligosaccharidyl-lipid Flippase (OLF) Family
  4. One (MVF) lipid-peptidoglycan precursor flippase involved in cell wall biosynthesis - (TC# 2.A.66.4) The Mouse Virulence Factor (MVF) Family
  5. One (AgnG) which includes a single functionally characterized member that extrudes the antibiotic, Agrocin 84 - (TC# 2.A.66.5) The Agrocin 84 Antibiotic Exporter (AgnG) Family
  6. And finally, one (Ank) that shuttles inorganic pyrophosphate (PPi) - (TC# 2.A.66.9) The Progressive Ankylosis (Ank) Family

Lysine Exporters are a superfamily of transmembrane proteins which export amino acids, lipids and heavy metal ions. They provide ionic homeostasis, play a role in cell envelope assembly, and protect from excessive concentrations of heavy metals in cytoplasm. The superfamily was named based on the early discovery of the LysE carrier protein of Corynebacterium glutamicum.

The Disufide bond oxidoreductase D (DsbD) family is a member of the Lysine Exporter (LysE) Superfamily. A representative list of proteins belonging to the DsbD family can be found in the Transporter Classification Base.

Divalent anion:Na+ symporters were found in bacteria, archaea, plant chloroplasts and animals.

The C4-dicarboxylate uptake family or Dcu family is a family of transmembrane ion transporters found in bacteria. Their function is to exchange dicarboxylates such as aspartate, malate, fumarate and succinate.

The arsenical resistance-3 (ACR3) family is a member of the BART superfamily. Based on operon analyses, ARC3 homologues may function either as secondary carriers or as primary active transporters, similarly to the ArsB and ArsAB families. In the latter case ATP hydrolysis again energizes transport. ARC3 homologues transport the same anions as ArsA/AB homologues, though ArsB homologues are members of the IT Superfamily and homologues of the ARC3 family are within the BART Superfamily suggesting they may not be evolutionarily related.

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The BlyA Holin Family is a group of holin proteins that are approximately 55-70 amino acyl residues (aas) in length and exhibit one transmembrane segment (TMS). A representative list of the proteins belonging to the BlyA holin family can be found in the Transporter Classification Database.

The Putative Archaeal 2 TMS Holin (A2-Hol) Family consists of a few putative holins from Thaumarchaeota ranging in size from about 130 to 165 amino acyl residues (aas) and exhibiting 2 transmembrane segments (TMSs). A representative list of proteins belonging to the A2-Hol family can be found in the Transporter Classification Database. The archaeon, Candidatus Nitrosoarchaeum limnia, encodes adjacent genes designated Toxin Secretion/Lysis Holin. The "toxin" gene encodes a soluble protein of 325 aas stated as belonging to the "Glycosyltransferase GBT-type Superfamily". This protein brings up other glycosyltransferases in a NCBI BLAST search. The adjacent gene encodes a small protein of 132 aas and 2 TMSs that could be a holin, based on its size and topology. This protein has the UniProt accession number of S2E3C4. Paralogues are found in this same organism and other closely related species.

The Na+-transporting Carboxylic Acid Decarboxylase (NaT-DC) Family (TC# 3.B.1) is a family of porters that belong to the CPA superfamily. Members of this family have been characterized in both Gram-positive and Gram-negative bacteria. A representative list of proteins belonging to the NaT-DC family can be found in the Transporter Classification Database.

Phosphate (Pho) Regulon

The Phosphate (Pho) regulon is a bacterial regulatory mechanism used for the conservation and management of inorganic phosphate within the cell. It was first discovered in Escherichia coli as an operating system for the bacterial strain, and was later identified in other species. The Pho system is composed of various components including extracellular enzymes and transporters that are capable of phosphate assimilation in addition to extracting inorganic phosphate from organic sources. This is an essential process since phosphate plays an important role in cellular membranes, genetic expression, and metabolism within the cell. Under low nutrient availability, the Pho regulon helps the cell survive and thrive despite a depletion of phosphate within the environment. When this occurs, phosphate starvation-inducible (psi) genes activate other proteins that aid in the transport of inorganic phosphate.

References

  1. ↑ Akahane, Shohei; Kamata, Hideaki; Yagisawa, Hitoshi; Hirata, Hajime (2003-02-01). "A novel neutral amino acid transporter from the hyperthermophilic archaeon Thermococcus sp. KS-1". Journal of Biochemistry. 133 (2): 173–180. doi:10.1093/jb/mvg021. ISSN   0021-924X. PMID   12761179.
  2. ↑ "2.A.95 The 6TMS Neutral Amino Acid Transporter (NAAT) Family". Transporter Classification Database. Retrieved 2016-02-25.
  3. ↑ Drew, David; Sjöstrand, Dan; Nilsson, Johan; Urbig, Thomas; Chin, Chen-ni; de Gier, Jan-Willem; von Heijne, Gunnar (2002-03-05). "Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis". Proceedings of the National Academy of Sciences of the United States of America. 99 (5): 2690–2695. Bibcode:2002PNAS...99.2690D. doi:10.1073/pnas.052018199. ISSN   0027-8424. PMC   122409 . PMID   11867724.

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