José de Jesús Olivares-Trejo

The pair of arginine codons AGA AGG close to the initiation codon of the lambda int gene inhibits cell growth and protein synthesis by accumulating peptidyl-tRNAArg4.

To analyse the mechanism by which rare codons near the initiation codon inhibit cell growth and protein synthesis, we used the bacteriophage lambda int gene or early codon substitution derivatives. The lambda int gene has a high frequency of rare ATA, AGA and AGG codons; two of them (AGA AGG) located at positions 3 and 4 of the int open reading frame (ORF). Escherichia coli pth (rap) cells, which are defective in peptidyl‐tRNA hydrolase (Pth) activity, are more susceptible to the inhibitory effects of int expression as compared with wild‐type cells. Cell growth and Int protein synthesis were enhanced by overexpression of Pth and tRNAArg4 cognate to AGG and AGA but not of tRNAIle2a specific for ATA. The increase of Int protein synthesis also takes place when the rare arginine codons AGA and AGG at positions 3 and 4 are changed to common arginine CGT or lysine AAA codons but not to rare isoleucine ATA codons. In addition, overexpression of int in Pth defective cells provokes accumulation of peptidyl‐tRNAArg4 in the soluble fraction. Therefore, cell growth and Int synthesis inhibition may be due to ribosome stalling and premature release of peptidyl‐tRNAArg4 from the ribosome at the rare arginine codons of the first tandem, which leads to cell starvation for the specific tRNA.

Streptococcus pneumoniae requires iron for its viability and expresses two membrane proteins that bind haemoglobin and haem

Streptococcus pneumoniae, a human pathogen bacterium, can support its growth using haemoglobin (Hb) and haem as sole iron sources, but not when holo-transferrin or holo-lactoferrin is supplied. For this reason, it is easy to think that the principal iron sources for this pathogen inside humans are Hb and haem. Unfortunately, the mechanism has been poorly studied. The findings presented in this study are the first efforts that attempted to explain the mechanism involved in iron acquisition of this pathogen. This pathogen was capable of supporting its viability when iron sources such as Hb or haem were supplied. Membranes of S. pneumoniae were separated and their respective proteins were solubilized in order to be purified by haem-affinity chromatography. This strategy allowed us to purify seven membrane proteins. An experiment of competence with haem and iron showed two potential haem and Hb-binding proteins. Their Hb-binding function was confirmed by overlay assay using Hb and their respective identities were obtained by mass spectrometry. Then by amino acid alignment analysis, the motif involved in binding of Hb or haem was revealed. These results are the first findings that attempt to explain the mechanisms developed by S. pneumoniae to acquire iron from Hb or haem in the host, which could allow a better understanding of the biology of this bacterium.

Helicobacter pylori secretes the chaperonin GroEL (HSP60), which binds iron

Helicobacter pylori is a bacterium that can use multiple iron sources. However, it is unknown whether this bacterium secretes molecules such as siderophores or haemophores to scavenge iron. Here, we report the first secreted iron‐binding protein of H. pylori, which we purified by haem‐affinity chromatography. Mass spectrometry analysis revealed its identity as chaperonin (HpGroEL). When we compared HpGroEL with EcGroEL from Escherichia coli, they were homologous, showing 60% similarity. Additionally, purified cytoplasmic HpGroEL could also bind iron. Perhaps H. pylori secretes HpGroEL to maintain the appropriate folding of extracellular proteins and to bind iron.

The gene frpB2 of Helicobacter pylori encodes an hemoglobin-binding protein involved in iron acquisition.

Human hemoglobin (Hb) is a metalloprotein used by pathogens as a source of iron during invasive process. It can support the Helicobacter pylori growth and several proteins are induced during iron starvation. However, the identity of those proteins remains unknown. In this work, by in silico analysis we identified FrpB2 in H. pylori genome. This protein was annotated as an iron-regulated outer membrane protein. Multiple amino acid alignment showed the motifs necessary for Hb-binding. We demonstrate the ability of FrpB2 to bind Hb by overlay experiments. In addition, the overexpression of this gene allowed the cell growth in media without free iron but supplemented with Hb. All these results support the idea that frpB2 is a gene of H. pylori involved in iron acquisition when Hb is used as a sole iron source.

Entamoeba histolytica TATA‐box binding protein binds to different TATA variants in vitro

The ability of Entamoeba histolytica TATA binding protein (EhTBP) to interact with different TATA boxes in gene promoters may be one of the key factors to perform an efficient transcription in this human parasite. In this paper we used several TATA variants to study the in vitro EhTBP DNA‐binding activity and to determine the TATA‐EhTBP dissociation constants. The presence of EhTBP in complexes formed by nuclear extracts (NE) and the TATTTAAA oligonucleotide, which corresponds to the canonical TATA box for E. histolytica, was demonstrated by gel‐shift assays. In these experiments a single NE‐TATTTAAA oligonucleotide complex was detected. Complex was retarded by anti‐EhTBP Igs in supershift experiments and antibodies also recognized the cross‐linked complex in Western blot assays. Recombinant EhTBP formed specific complexes with TATA variants found in E. histolytica gene promoters and other TATA variants generated by mutation of TATTTAAA sequence. The dissociation constants of recombinant EhTBP for TATA variants ranged between 1.04 (±0.39) × 10−11 and 1.60 (±0.37) × 10−10 m. TATTTAAA and TAT_ _AAA motifs presented the lowest KD values. Intriguingly, the recombinant EhTBP affinity for TATA variants is stronger than other TBPs reported. In addition, EhTBP is more promiscuous than human and yeast TBPs, probably due to modifications in amino acids involved in TBP‐DNA binding.

Cloning and identification of a gene coding for a 26-kDa hemoglobin-binding protein from Entamoeba histolytica.

The capability of Entamoeba histolytica to use hemoglobin (Hb) as an iron source has been documented. However, the underlying mechanism to acquire iron from this source is poorly understood. In the present work, an in silico analysis in the E. histolytica genome (Pathema database) allowed us to identify a gene coding for a putative 26-kDa protein (Ehhmbp26) which contains the motifs necessary for Hb-binding. The purified Ehhmbp26 protein was able to bind Hb. Albeit with less efficiency, trophozoites were able to grow using Hb as the only iron source. In addition, ehhmbp26 RNA and the Ehhmbp26 protein were only expressed under iron restrictive conditions and ehhmbp26 RNA was subsequently inhibited after iron supplementation indicating that ehhmbp26 gene is negatively regulated by iron. These results suggest that the Ehhmbp26 protein may be involved in a mechanism by which E. histolytica scavenges iron from Hb.

Ehhmbp45 is a novel hemoglobin-binding protein identified in Entamoeba histolytica

Hemoglobin‐binding proteins are necessary for pathogens to obtain iron from Hb. Entamoeba histolytica can grow using Hb as source of iron, but the underlying mechanism has not previously been established. In this work, we identified a 45 kDa Hb‐binding protein of E. histolytica, which we named Ehhmbp45. In silico analysis showed that Ehhmbp45 contains the conserved domains needed for Hb‐binding, while overlay assays demonstrated that Ehhmbp45 is able to bind Hb. In addition, we found that Ehhmbp45 mRNA levels were up‐regulated under iron starvation conditions and were subsequently restored to basal levels when Hb was added to the cell cultures. These findings provide the first insights on the role of Ehhmbp45 in iron acquisition from Hb.

Entamoeba histolytica secretes two haem-binding proteins to scavenge haem.

Entamoeba histolytica is a human pathogen which can grow using different sources of iron such as free iron, lactoferrin, transferrin, ferritin or haemoglobin. In the present study, we found that E. histolytica was also capable of supporting its growth in the presence of haem as the sole iron supply. In addition, when trophozoites were maintained in cultures supplemented with haemoglobin as the only iron source, the haem was released and thus it was introduced into cells. Interestingly, the Ehhmbp26 and Ehhmbp45 proteins could be related to the mechanism of iron acquisition in this protozoan, since they were secreted to the medium under iron-starvation conditions, and presented higher binding affinity for haem than for haemoglobin. In addition, both proteins were unable to bind free iron or transferrin in the presence of haem. Taken together, our results suggest that Ehhmbp26 and Ehhmbp45 could function as haemophores, secreted by this parasite to facilitate the scavenging of haem from the host environment during the infective process.

The frpB1 gene of Helicobacter pylori is regulated by iron and encodes a membrane protein capable of binding haem and haemoglobin

FrpB1 is a novel membrane protein of Helicobacter pylori that is capable of binding both haem and haemoglobin but consistently shows more affinity for haem. The mRNA levels of frpB1 were repressed by iron and lightly modulated by haem or haemoglobin. The overexpression of the frpB1 gene supported cellular growth when haem or haemoglobin were supplied as the only iron source. Three‐dimensional modelling revealed the presence of motifs necessary to bind either haem or haemoglobin. Our overall results support the idea that FrpB1 is a membrane protein of H. pylori that allows this pathogen to survive in the human stomach.

Entamoeba histolytica: A unicellular organism containing two active genes encoding for members of the TBP family

Entamoeba histolytica is the protozoan parasite which causes human amoebiasis. In this parasite, few encoding genes for transcription factors have been cloned and characterized. The E. histolytica TATA-box binding protein (EhTBP) is the first basal transcription factor that has been studied. To continue with the identification of other members of the basal transcription machinery, we performed an in silico analysis of the E. histolytica genome and found three loci encoding for polypeptides with similarity to EhTBP. One locus has a 100% identity to the previously Ehtbp gene reported by our group. The second locus encodes for a 212 aa polypeptide that is 100% identical to residues 23-234 from EhTBP. The third one encodes for a 216 aa polypeptide of 24kDa that showed 42.6% identity and 73.7% similarity to EhTBP. This protein was named E. histolytica TBP-related factor 1 (EhTRF1). Ehtrf1 gene was expressed in bacteria and the purified 28kDa recombinant polypeptide showed the capacity to bind to TATTTAAA-box by electrophoretic mobility shift assays. K(D) values for rEhTBP and rEhTRF1 were (1.71+/-2.90)x10(-12)M and (1.12+/-0.160)x10(-11)M, respectively. Homology modeling of EhTRF1 and EhTBP revealed that, although they were very similar, they showed some differences on their surfaces. Thus, E. histolytica is a unicellular organism having two members of the TBP family.