Genome-wide investigation of the LARP gene family: focus on functional identification and transcriptome profiling of ZmLARP6c1 in maize pollen

BACKGROUND

The La-related proteins (LARPs) are a superfamily of RNA-binding proteins associated with regulation of gene expression. Evidence points to an important role for post-transcriptional control of gene expression in germinating pollen tubes, which could be aided by RNA-binding proteins.

RESULTS

In this study, a genome-wide investigation of the LARP proteins in eight plant species was performed. The LARP proteins were classified into three families based on a phylogenetic analysis. The gene structure, conserved motifs, cis-acting elements in the promoter, and gene expression profiles were investigated to provide a comprehensive overview of the evolutionary history and potential functions of ZmLARP genes in maize. Moreover, ZmLARP6c1 was specifically expressed in pollen and ZmLARP6c1 was localized to the nucleus and cytoplasm in maize protoplasts. Overexpression of ZmLARP6c1 enhanced the percentage pollen germination compared with that of wild-type pollen. In addition, transcriptome profiling analysis revealed that differentially expressed genes included PABP homologous genes and genes involved in jasmonic acid and abscisic acid biosynthesis, metabolism, signaling pathways and response in a Zmlarp6c1::Ds mutant and ZmLARP6c1-overexpression line compared with the corresponding wild type.

CONCLUSIONS

The findings provide a basis for further evolutionary and functional analyses, and provide insight into the critical regulatory function of ZmLARP6c1 in maize pollen germination.

Predictors of Urinary Continence Recovery after Laparoscopic-Assisted Radical Prostatectomy: Is Surgical Urethral Length the Only Key Factor?

Several efforts in recent years have been made to predict urinary continence (UC) recovery after radical prostatectomy. The aim of our study was to investigate the impact of surgical urethral length preservation (SULP) on urinary continence after LARP (laparoscopic-assisted radical prostatectomy). We retrospectively queried our datasets from May 2021 to May 2022. After the application of exclusion criteria, a total of 100 patients who underwent LARP for prostate cancer at our institution were enrolled. Through a sterile ruler inserted by a 12 mm trocar, the length of the membranous urethra spared during LARP was assessed intra-operatively. The baseline and peri- and postoperative data of patients were collected, and UC was defined as 0 or 1 on a safety pad. The median SULP was 20.5 mm (IQR, 14.5-25), and the median intraoperative EBL were 150 mL (IQR, 100-200). The Kaplan-Meier curve showed a significant difference at 20 mm, which was used as the cut-off value for SULP (log-rank test, p < 0.001). Multivariate Cox proportional hazards models showed that SULP and EBL < 250 mL were associated with UC recovery (all p < 0.02). Surgical urethral length preservation seemed to improve early UC recovery after LARP. Further multicentric studies are needed to confirm our findings.

Is it possible to diagnose Posterior Semicircular Canal BPPV from the sitting position? The role of the Head Pitch Test and the upright tests along the RALP and LARP planes

PURPOSE

The diagnosis of benign paroxysmal positional vertigo (BPPV) involving the posterior semicircular canal (PSC) is traditionally entrusted to positioning tests where patients are rapidly brought in the supine position. This prospective study aims to define the role of a diagnostic protocol for PSC-BPPV including only upright tests.

MATERIALS AND METHODS

109 patients with PSC-BPPV were enrolled. The Head Pitch Test (HPT) was carried out first. If uneventful, the patient's head was turned 45° to each side and bent back-and-forth along the plane aligning either with the right anterior-left posterior (RALP) or left anterior-right posterior (LARP) canals, thus performing the upright RALP / upright LARP (uRALP/uLARP) test. Nystagmus observed was used to predict the diagnosis, which was therefore confirmed by Dix-Hallpike tests.

RESULTS

PSC-BPPV could be correctly diagnosed in 75.2% of cases with the sole HPT and in 87.2% of cases by adding the uRALP/uLARP test (Upright Protocol). The time elapsed from symptoms onset was closely related to the protocol sensitivity, as it reached 100% (64/64) in acute patients while decreased to 68.9% (31/45) in cases evaluated after 7 days (p < 0.001).

CONCLUSIONS

Upright maneuvers could correctly diagnose PSC-BPPV in most cases. uRALP/uLARP test demonstrated to improve the sensitivity of the HPT, mainly in recent-onset BPPV.

vHIT Testing of Vertical Semicircular Canals With Goggles Yield Different Results Depending on Which Canal Plane Being Tested

Objective: The use of goggles to assess vertical semicircular canal function has become a standard method in vestibular testing, both in clinic and in research, but there are different methods and apparatus in use. The aim of this study was to determine what the cause of the systematic differences is between gain values in testing of the vertical semicircular canals with two different video head impulse test (vHIT) equipment in subjects with normal vestibular function. Study Design: Retrospective analysis of gain values on patients with clinically deemed normal vestibular function (absence of a corrective eye saccade), tested with either Interacoustics or Otometrics system. Prospective testing of subjects with normal vestibular function with the camera records the eye movements of both eyes. Finally, 3D sensors were placed on different positions on the goggles measuring the actual vertical movement in the different semicircular planes. Results: In the clinical cohorts, the gain depended on which side and semicircular canal was tested (p < 0.001). In the prospective design, the combination between the stimulated side, semicircular canal, and position of the recording device (right/left eye) highly influenced the derived gain (p < 0.001). The different parts of the goggles also moved differently in a vertical direction during vertical semicircular canal testing. Conclusion: The gain values when testing the function of the vertical semicircular canals seem to depend upon which eye is recorded and which semicircular plane is tested and suggests caution when interpreting and comparing results when different systems are used both clinically as well as in research. The results also imply that further research and development are needed to obtain accurate vertical semicircular canal testing, in regard to both methodology and equipment design.

Controversies around the function of LARP1

The RNA-binding protein LARP1 has generated interest in recent years for its role in the mTOR signalling cascade and its regulation of terminal oligopyrimidine (TOP) mRNA translation. Paradoxically, some scientists have shown that LARP1 represses TOP translation while others that LARP1 activates it. Here, we present opinions from four leading scientists in the field to discuss these and other contradictory findings.

Distribution, organization an evolutionary history of La and LARPs in eukaryotes

The fate of any cellular RNA is largely influenced by the nature and diversity of its interactions with various RNA-binding proteins (RBPs) leading to the formation of a biologically significant ribonucleoprotein (RNP) complex. La motif-containing proteins (composed of genuine La and La-related proteins (LARPs)) represent an evolutionary conserved family of RBPs that encompass a large range of crucial functions, involving coding and non-coding RNAs. In this work, we provide data that extend our previous knowledge on the distribution, organization and evolutionary history of this important protein family. Using a repertoire of 345 La motif-containing proteins from 135 species representing all major eukaryotic lineages, we were able to pinpoint many lineage-specific variations in the structural organization of La and LARPs and propose new evolutive scenarios to explain their modern genomic distribution.

Functional and Structural Aspects of La Protein Overexpression in Lung Cancer

La is an abundant phosphoprotein that protects polymerase III transcripts from 3'-5' exonucleolytic degradation and facilitates their folding. Consisting of the evolutionary conserved La motif (LAM) and two consecutive RNA Recognition Motifs (RRMs), La was also found to bind additional RNA transcripts or RNA domains like internal ribosome entry site (IRES), through sequence-independent binding modes which are poorly understood. Although it has been reported overexpressed in certain cancer types and depletion of its expression sensitizes cancer cells to certain chemotherapeutic agents, its role in cancer remains essentially uncharacterized. Herein, we study the effects of La overexpression in A549 lung adenocarcinoma cells, which leads to increased cell proliferation and motility. Expression profiling of several transcription and translation factors indicated that La overexpression leads to downregulation of global translation through hypophosphorylation of 4E-BPs and upregulation of IRES-mediated translation. Moreover, analysis of La localization after nutrition deprivation of the transfected cells showed a normal distribution in the nucleus and nucleoli. Although the RNA binding capacity of La has been primarily linked to the synergy between the conserved LAM and RRM1 domains which act as a module, we show that recombinant stand-alone LAM can specifically bind a pre-tRNA ligand, based on binding experiments combined with NMR analysis. We propose that LAM RNA binding properties could support the expanding and diverse RNA ligand repertoire of La, thus promoting its modulatory role, both under normal and pathogenic conditions like cancer.

pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins

La-related proteins 7 (LARP7) are a class of RNA chaperones that bind the 3' ends of RNA and are constitutively associated with their specific target RNAs. In metazoa, Larp7 binds to the long non-coding 7SK RNA as a core component of the 7SK RNP, a major regulator of eukaryotic transcription. In the ciliate Tetrahymena the LARP7 protein p65 is a component of telomerase, an essential ribonucleoprotein complex that maintains the telomeric DNA at eukaryotic chromosome ends. p65 is important for the ordered assembly of telomerase RNA (TER) with telomerase reverse transcriptase. Unexpectedly, Schizosaccharomyces pombe Pof8 was recently identified as a LARP7 protein and a core component of fission yeast telomerase essential for biogenesis. LARP7 proteins have a conserved N-terminal La motif and RRM1 (La module) and C-terminal RRM2 with specific RNA substrate recognition attributed to RRM2, first structurally characterized in p65 as an atypical RRM named xRRM. Here we present the X-ray crystal structure and NMR studies of S. pombe Pof8 RRM2. Sequence and structure comparison of Pof8 RRM2 to p65 and human Larp7 xRRMs reveals conserved features for RNA binding with the main variability in the length of the non-canonical helix α3. This study shows that Pof8 has conserved xRRM features, providing insight into TER recognition and the defining characteristics of the xRRM.

Role of the RNA-binding protein La in cancer pathobiology

RNA-binding proteins are important regulators of RNA metabolism and are of critical importance in all steps of the gene expression cascade. The role of aberrantly expressed RBPs in human disease is an exciting research field and the potential application of RBPs as a therapeutic target or a diagnostic marker represents a fast-growing area of research.Aberrant overexpression of the human RNA-binding protein La has been found in various cancer entities including lung, cervical, head and neck, and chronic myelogenous leukaemia. Cancer-associated La protein supports tumour-promoting processes such as proliferation, mobility, invasiveness and tumour growth. Moreover, the La protein maintains the survival of cancer cells by supporting an anti-apoptotic state that may cause resistance to chemotherapeutic therapy.The human La protein represents a multifunctional post-translationally modified RNA-binding protein with RNA chaperone activity that promotes processing of non-coding precursor RNAs but also stimulates the translation of selective messenger RNAs encoding tumour-promoting and anti-apoptotic factors. In our model, La facilitates the expression of those factors and helps cancer cells to cope with cellular stress. In contrast to oncogenes, able to initiate tumorigenesis, we postulate that the aberrantly elevated expression of the human La protein contributes to the non-oncogenic addiction of cancer cells. In this review, we summarize the current understanding about the implications of the RNA-binding protein La in cancer progression and therapeutic resistance. The concept of exploiting the RBP La as a cancer drug target will be discussed.

Potential oligogenic disease of mental retardation, short stature, spastic paraparesis, and osteopetrosis

The interaction of multiple genetic factors, as opposed to monogenic inheritance, has been suspected to play a role in many diseases. This interaction has been described as an oligogenic inheritance model, which may be a useful tool in explaining certain clinical observations. The purpose of this study was to search for novel genetic defects among members of a family with traits that include mental retardation, short stature, osteopetrosis, calcification of basal ganglia, and thinning of the corpus callosum. In the index case (111-4), we identified four homozygous mutations: chromosome 8, intron2 (c.232+1G>A) at CA2 gene; chromosome 15, exon 32 (c.6100C>T) at the SPG11; chromosome 5, exon 11 (c.1015G>A) at the MCCC2; and chromosome 9, exon 9 (C.1193g>t) at the LARP gene. The mutations were confirmed by Sanger sequencing, and both parents were observed to be heterozygous for the four mutations. A moderately affected sister of the index case was homozygous for only three mutations in CA2, LARP, and Mccc2, while a nonaffected sister was heterozygous for three mutations in CA2, LARP, and MCCC2 and negative for SPG11. The clinical features of the two affected sisters can be explained distinctively by each homozygous mutation in an oligogenic pattern of inheritance. This family represents an example of an oligogenic pattern of inheritance of mental retardation, short stature, spastic paraparesis, and osteopetrosis.

SUMO Modification of the RNA-Binding Protein La Regulates Cell Proliferation and STAT3 Protein Stability

The cancer-associated RNA-binding protein La is posttranslationally modified by phosphorylation and sumoylation. Sumoylation of La regulates not only the trafficking of La in neuronal axons but also its association with specific mRNAs. Depletion of La in various types of cancer cell lines impairs cell proliferation; however, the molecular mechanism whereby La supports cell proliferation is not clearly understood. In this study, we address the question of whether sumoylation of La contributes to cell proliferation of HEK293 cells. We show that HEK293 cells stably expressing green fluorescent protein (GFP)-tagged wild-type La (GFP-La^WT) grow faster than cells expressing a sumoylation-deficient mutant La (GFP-La^SD), suggesting a proproliferative function of La in HEK293 cells. Further, we found that STAT3 protein levels were reduced in GFP-La^SD cells due to an increase in STAT3 ubiquitination and that overexpression of STAT3 partially restored cell proliferation. Finally, we present RNA sequencing data from RNA immunoprecipitations (RIPs) and report that mRNAs associated with the cell cycle and ubiquitination are preferentially bound by GFP-La^WT and are less enriched in GFP-La^SD RIPs. Taken together, results of our study support a novel mechanism whereby sumoylation of La promotes cell proliferation by averting ubiquitination-mediated degradation of the STAT3 protein.

Assessment of VOR gain function and its test-retest reliability in normal hearing individuals

Video head impulse test (vHIT) aids to assess all three pairs of semi-circular canals (SCCs) separately and can be utilized to find out the exact site of lesion in any three SCCs by measuring vestibulo ocular reflex (VOR) gain. VOR gain value of vHIT has been used to diagnose different vestibular pathologies. Hence, it is important to establish the test-retest reliability of the VOR gain parameters before it could be administered to the patients. Therefore, the aim of the present study was to obtain VOR gain data, correlate all planes in both sides of head (right and left) and assess the test-retest reliability of VOR gain measure using vHIT in 25 normal young adult participants. Video head impulse test tests were carried out with prototype ICS impulse video goggles with a camera speed of 250 frames/s, recording motion of the right eye in all three planes (lateral, right anterior left posterior, left anterior right posterior) for all the participants. vHIT testing was repeated for all the participants after 15 days. Statistical analysis revealed that mean VOR gain for right horizontal canal was higher than the left horizontal canal; right anterior canal was higher than left anterior canal and left anterior was higher than right posterior canal. Horizontal canals have more gain compared to anterior and posterior canals. There was no significant difference between the VOR gain of session 1 and session 2 for each SCC.

The La-Related Proteins, a Family with Connections to Cancer

The evolutionarily-conserved La-related protein (LARP) family currently comprises Genuine La, LARP1, LARP1b, LARP4, LARP4b, LARP6 and LARP7. Emerging evidence suggests each LARP has a distinct role in transcription and/or mRNA translation that is attributable to subtle sequence variations within their La modules and specific C-terminal domains. As emerging research uncovers the function of each LARP, it is evident that La, LARP1, LARP6, LARP7 and possibly LARP4a and 4b are dysregulated in cancer. Of these, LARP1 is the first to be demonstrated to drive oncogenesis. Here, we review the role of each LARP and the evidence linking it to malignancy. We discuss a future strategy of targeting members of this protein family as cancer therapy.